From bee9e21897cd54ddad2cd2b22e7e31e083ebc980 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Mon, 22 Sep 2014 16:14:19 +0100
Subject: [PATCH] ENSCORESW-524: coordinate overlap on refseq_import gene set
include alternative sequences with correct start/end
---
.../xref_mapping/XrefParser/RefSeqCoordinateParser.pm | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm
index d23d3ceeda..4cdcd2ebce 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm
@@ -179,13 +179,13 @@ sub run_script {
my $sa = $core_dba->get_SliceAdaptor();
my $sa_of = $otherf_dba->get_SliceAdaptor();
- my $chromosomes_of = $sa_of->fetch_all('chromosome');
+ my $chromosomes_of = $sa_of->fetch_all('chromosome', undef, 1);
# Fetch analysis object for refseq
my $aa_of = $otherf_dba->get_AnalysisAdaptor();
my $logic_name;
foreach my $ana(@{ $aa_of->fetch_all() }) {
- if ($ana->logic_name =~ /refseq_[a-z]+_import/) {
+ if ($ana->logic_name =~ /refseq_import/) {
$logic_name = $ana->logic_name;
}
}
@@ -224,7 +224,7 @@ sub run_script {
}
# Fetch slice in core database which overlaps refseq transcript
- my $chromosome = $sa->fetch_by_region('chromosome', $chr_name, $transcript_of->start, $transcript_of->end);
+ my $chromosome = $sa->fetch_by_region('chromosome', $chr_name, $transcript_of->seq_region_start, $transcript_of->seq_region_end);
my $transcripts = $chromosome->get_all_Transcripts(1);
# Create a range registry for all the exons of the ensembl transcript
--
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